Research Article

Atomic-Level Characterization of the Structural Dynamics of Proteins

See allHide authors and affiliations

Science  15 Oct 2010:
Vol. 330, Issue 6002, pp. 341-346
DOI: 10.1126/science.1187409

You are currently viewing the abstract.

View Full Text


Molecular dynamics (MD) simulations are widely used to study protein motions at an atomic level of detail, but they have been limited to time scales shorter than those of many biologically critical conformational changes. We examined two fundamental processes in protein dynamics—protein folding and conformational change within the folded state—by means of extremely long all-atom MD simulations conducted on a special-purpose machine. Equilibrium simulations of a WW protein domain captured multiple folding and unfolding events that consistently follow a well-defined folding pathway; separate simulations of the protein’s constituent substructures shed light on possible determinants of this pathway. A 1-millisecond simulation of the folded protein BPTI reveals a small number of structurally distinct conformational states whose reversible interconversion is slower than local relaxations within those states by a factor of more than 1000.

View Full Text